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In some older treatments of the family, Berberidaceae only included four genera (Berberis, Epimedium, Mahonia, Vancouveria), with the other genera treated in separate families, Leonticaceae (Bongardia, Caulophyllum, Gymnospermium, Leontice), Nandinaceae (Nandina), and Podophyllaceae (Achlys, Diphylleia, Dysosma, Jeffersonia, Podophyllum, Ranzania).

Mahonia is very closely related to Berberis, and most botanists now include it in Berberis. Species in the two genera can be hybridised, with the hybrids being classified in the (now superfluous) hybrid genus × Mahoberberis. Diphyllaea is closely related or perhaps paraphyletic or embedded in Podophyllum, and instead of the current trend to subdivide Podophyllum into Dysosma and Sinopodophyllum, inclusion of Diphyllaea in Podophyllum is equally warranted.